Welcome to BRAD: Bioinformatics Retrieval Augmented Data’s documentation!

Contents:

• About BRAD
  • Vision
  • Key Features
  • Future Work
• Interface
  • Quickstart
    • Running BRAD from the CLI
    • Available Methods
    • chat()
  • Agent Class
    • Main Methods
    • State Schema
    • Class Methods
    • Agent
    • AgentFactory
  • Agents as LLMs
    • bot
    • _call()
    • _llm_type()
  • Graphical User Interface (GUI)
    • React GUI
    • Flask API
    • configure_RAG_contextualCompression()
    • configure_RAG_numberArticles()
    • configure_RAG_searchMechanism()
    • databases_available()
    • databases_create()
    • databases_set()
    • initiate_start()
    • invoke()
    • llm_apikey()
    • llm_get()
    • llm_set()
    • sessions_change()
    • sessions_create()
    • sessions_open()
    • sessions_remove()
    • sessions_rename()
    • set_global_output_path()
    • validate_database_name()
  • Configurations
• Core Modules
  • Large Language Models
    • Available LLMs
    • Loading LLMs
    • llm_switcher()
    • load_llama()
    • load_nvidia()
    • load_openai()
  • Logging
    • Log Format
    • Log Methods
    • debugLog()
    • errorLog()
    • is_json_serializable()
    • llmCallLog()
    • loadFileLog()
    • logger()
    • userOutput()
  • Utilities
    • Scope
    • Available Methods
    • add_output_file_path_to_string()
    • compile_latex_to_pdf()
    • delete_dirs_without_log()
    • ensure_directory_exists()
    • fieldSelectorFromDataFrame()
    • find_integer_in_string()
    • loadFromFile()
    • load_file_to_dataframe()
    • makeNamesConsistent()
    • outputFiles()
    • outputFromPriorStep()
    • pdfDownloadPath()
    • save()
    • savefig()
    • strip_root_path()
    • word_similarity()
  • Planner
    • displayPipeline2User()
    • getKnownPipelines()
    • planner()
    • response2processes()
  • Routing
    • Scope
    • Available Methods
    • add_sentence()
    • buildRoutes()
    • getRouter()
    • getRouterPath()
    • read_prompts()
    • reroute()
  • Prompt Templates
    • fieldChooserTemplate()
    • fileChooserTemplate()
    • geneDatabaseCallerTemplate()
    • geneDatabaseLLMreply()
    • getPythonEditingTemplate()
    • get_default_context()
    • history_chat_template()
    • matlabPromptTemplate()
    • plannerEditingTemplate()
    • plannerTemplate()
    • plannerTemplateForLibrarySelection()
    • pythonPromptTemplate()
    • pythonPromptTemplateWithFiles()
    • rerouteTemplate()
    • scrapeTemplate()
    • scriptSelectorTemplate()
    • setReportTitleTemplate()
    • summarizeAnalysisPipelineTemplate()
    • summarizeDatabaseCallerTemplate()
    • summarizeRAGTemplate()
    • summarize_code_template()
    • summarize_document_template()
• Tool Modules
  • Lab Notebook
    • Key Functions
    • Available Methods
    • adj_matrix_builder()
    • best_match()
    • contextual_compression()
    • create_database()
    • cut()
    • documentEnrichment()
    • getDocumentSimilarity()
    • getInputDocumentJSONs()
    • getPreviousInput()
    • get_all_sources()
    • get_wordnet_pos()
    • normalize_adjacency_matrix()
    • pagerank_rerank()
    • pagerank_weighted()
    • queryDocs()
    • relative_frequency_of_char()
    • remove_repeats()
    • retrieval()
  • Digital Library
    • Literature Repositories
    • arxiv()
    • arxivStageOne()
    • arxivStageTwo()
    • arxiv_scrape()
    • arxiv_search()
    • biorxiv()
    • biorxiv_real_search()
    • create_db()
    • parse_llm_response()
    • pubmed()
    • result_set_to_string()
    • search_pubmed_article()
    • set_arxiv_df_display()
    • updateDatabase()
    • webScraping()
    • webScrapingStageOne()
    • webScrapingStageTwo()
    • Bioinformatics Database
    • geneDBRetriever()
    • getTablesFormatting()
    • parse_llm_response()
    • Enrichr
    • queryEnrichr()
    • Gene Ontology (GO)
    • annotations()
    • chartGO()
    • fetch_annotation()
    • geneOntology()
    • goSearch()
    • pubmedPaper()
    • textGO()
  • Software
    • Code Caller
    • code_caller()
    • executeCode()
    • summarize_code_execution_results()
    • Python Codes
    • callPython()
    • editPythonCode()
    • execute_python_code()
    • extract_python_code()
    • find_closest_function()
    • find_py_files()
    • get_arguments_from_code()
    • get_py_description()
    • has_unclosed_symbols()
    • read_python_docstrings()
• Software Installation and Requirements
  • Software Requirements
    • Dependencies
  • Pip Installation
  • Conda Instillation
  • Docker Instillation

Indices and tables

• Module Index

• Search Page